User talk:Boghog

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Variability in PSA Measurement[edit]

I have edited it just because it is a very common problem occuring in practice. The review artcile may not be upto date but it is addressed considering routine problem of clinicains and lab professionals.

Arachidonate 15-lipoxygenase vs ALOX15[edit]

Hey Boghog - I started working on an eoxin article (from my userspace for now... User:Seppi333/Eoxin) and noticed an issue with the naming convention of the associated enzyme articles for these compounds. Arachidonate 15-lipoxygenase (15-LOX) has 2 subtypes: 15-LOX-1 (located at ALOX15 - this is the eoxin producing enzyme) and 15-LOX-2 (located at ALOX15B).

Our other lipoxygenase articles use the longer name (e.g., the most notable lipoxygenase is 5-LOX; this contraction and ALOX5 both redirect to Arachidonate 5-lipoxygenase), so I'm assuming the ALOX articles should be moved for consistency:

Do these moves seem appropriate? Also, should the general 15-LOX article be converted to a set index of these two, or just remain as is?

Seppi333 (Insert  | Maintained) 00:59, 5 January 2015 (UTC)

Some refs for context:

Hi Seppi333. The usual convention is to gene/protein articles using the approved HUGO gene symbol or recommend UniProt name. According to this convention, the two articles should be renamed as follows:
The complication is Arachidonate 15-lipoxygenase already exists as an enzyme article and IMHO should remain as is. Furthermore since ALOX15 and ALOX15B share the same EC number, it would not be appropriate to merge ALOX15 with Arachidonate 15-lipoxygenase. We could label the two isozymes "A" and "B" respectively, but ALOX15 is not normally referred to as the "A" isozyme. So I guess your proposal is the most reasonable, since these names correspond to the UniProt "expanded short names", 15-LOX-1 and 15-LOX-2, respectively. Boghog (talk) 01:26, 5 January 2015 (UTC)
Thanks for the clarification. So, should we use 1 and 2 or A and B following "Arachidonate 15-lipoxygenase" in the page names?
I also have a chemistry question that I need some clarification on. Most papers I've read indicate 5-LOX and 15-LOX metabolize along distinct but analogous pathways following synthesis by the associated 5-LOX or 15-LOX enzyme (see page 122 of the "15-LOX-1 review" pdf located here). However, reactome is indicating that EXA4 is produced from LTA4 via 15-LOX-1 in humans (the mostly complete series of reactions along arachidonic acid pathways is also located at special:Permalink/641335373#Biochemistry). I'm confused - wouldn't 15-lipoxygenase-1 action on LTA-4 create a completely different compound than EXA4 (aka 14,15-LTA4), or is that posible/correct? Seppi333 (Insert  | Maintained) 01:17, 7 January 2015 (UTC)
@Seppi333: Sorry for not responding sooner. You are asking interesting but challenging questions. Also arachidonic signaling is somewhat outside my area of expertise. Finally, I becoming somewhat burned out lately ;-) Regarding your first question, the existing nomenclature used by UniProt unfortunately does not provide a clean answer. In analogy to the 15-LOX-1 and 15-LOX-2 short names that are already in use, my suggestion is to use 1 and 2 following "Arachidonate 15-lipoxygenase" in article names. Regarding your second question, the "15-LOX-1 review" (secondary source) is correct and the reactome (tertiary source) is incorrect. It looks like the reactome misinterpreted PubMed (Figure 3) which was trying to distinguish (i) "5-LO-derived cysteinyl LTs" from (ii) "cysteinyl 14,15-LTs (EXs)". This distinction is important in interpreting mass spectral data but in no way should be interpreted as the two species interconverting as apparently the reactome database did.

Nevermind, I'm not going to edit these pages further since I lack the background chem knowledge to really understand what I'm writing about. And on that note...

Science Barnstar Hires.png The Science Barnstar
This is for all the work you put into expanding and improving amphetamine's chem content and citations; you helped a lot with getting through the FA process and I appreciate the assistance. Seppi333 (Insert  | Maintained) 01:48, 2 February 2015 (UTC)
Nada. My contribution was very minor. Kudos to you for your enormous hard work and determination in promoting amphetamine to FA status. Boghog (talk) 18:40, 2 February 2015 (UTC)

Replacing Cite PMID with Cite Journal[edit]

Can we have a bot do this on all medical articles and than do so again on regular basis?

Consensus is here [1] Doc James (talk · contribs · email) 05:26, 25 January 2015 (UTC)

Let me know if you are able to take this on? Happy to help with the bot approval process. Doc James (talk · contribs · email) 09:51, 31 January 2015 (UTC)
Sent you an email. Let me know if you are able to work on this? Doc James (talk · contribs · email) 04:03, 4 February 2015 (UTC)
@Doc James: Yes, I can start to work on this. However it would really be helpful if USER:Citation bot in the future would insert the full citation within the article instead of creating additional {{cite pmid}} templates. That way, we would only need to run the substitution bot once. Per consensus, we would seem to have the authority to request this. The problem is that USER:Citation bot is no longer actively maintained. I filed this bug report bug report last October and still no response. Thoughts? Boghog (talk) 20:55, 5 February 2015 (UTC)
A solution is we block USER:Citation bot and replace it with a bot that does what we wish. What do you think? Doc James (talk · contribs · email) 01:22, 6 February 2015 (UTC)
Blocking citation bot is not a good answer. The RFC linked above applies only to medical articles. A solution that better addresses the RFC would be to create a new bot that carries out the RFC's result only on medical articles. The new bot could also tag articles within the project to prevent citation bot from editing those articles if there is consensus within the project to do so. – Jonesey95 (talk) 03:10, 6 February 2015 (UTC)
This consensus was not limited to medical articles. One thing that bot approval group doesn't like is conflicting bots. I can bring this issue up with them when I apply for the approval of the new bot. Boghog (talk) 09:18, 6 February 2015 (UTC)
Perfect. Doc James (talk · contribs · email) 11:39, 7 February 2015 (UTC)

tools.wmflabs.org/citation-template-filling isn't running[edit]

Manage link if it should be & something has expired. RDBrown (talk) 04:19, 31 January 2015 (UTC)

Fixed Thanks for the alert. I have no idea why it was no longer running. I stopped and restarted the citation-template-filling webservice and it now runs again. Boghog (talk) 08:17, 31 January 2015 (UTC)

Nomination for merging of Template:Infobox nonhuman protein[edit]

Template:Infobox nonhuman protein has been nominated for merging with Template:Infobox protein. You are invited to comment on the discussion at the template's entry on the Templates for discussion page. Thank you. Andy Mabbett (Pigsonthewing); Talk to Andy; Andy's edits 16:33, 31 January 2015 (UTC)

Fine points of formatting citation template fields[edit]

Hi, Boghog,

I see you have been in the thick of editor discussions about how to format citation templates. I just saw your recent edit of Chikungunya on my watchlist, and looked up your wikilinks to editor discussion about the doi templates and other templates. Here on your talk page I see you are also discussing templates. I'd like my practice to human-readable, not subject to willy-nilly reversion by people running bots, and consistent with the practice of more experienced Wikipedians, so I'd appreciate hearing from you your thoughts on why (or why) to include whitespace between the equal sign that distinguishes a field label from field content or whitespace before or after the pipe character that shows the beginning of a new field. I have a habitual pattern in using whitespace, which I think I picked up from the documentation of the citation templates, but maybe I can change my habits if I see a rationale for doing so. For an example of how I do citation template, I invite you take a look at a Intelligence citations bibliography I keep in my user space. What do you think about the mark-up style there, which I tend to copy and paste into articles as occasion arises? Thanks for any thoughts you have about this or any pointers you can give to Wikipedia documentation on the issue. See you on the wiki. -- WeijiBaikeBianji (talk, how I edit) 00:14, 1 February 2015 (UTC)

Hi WeijiBaikeBianji. Thank you for your message. Concerning whether or not to pad template parameters with white space is purely a personal preference and is subject to WP:CITEVAR. There is a tradeoff between readability and compactness. Arguably the most readable templates have each parameter on its own line (vertical format). On the other hand, compactness is important if the citations are included in-line. Vertical formatted citations overwhelm the surrounding wiki text making it harder to edit. My personal opinion is that padding parameters with white space while retaining horizontal format is a good compromise between readability and compactness. Others may disagree. The reason I included white space in my recent edit to Chikungunya was that the script that I was using rebuilt the citation templates from scratch. The advantage of this is approach is consistency, the danger is that it may run afoul of WP:CITEVAR. Making edits only to add/subtract white space is generally frowned upon. Another concern that I have is the use of first1, last1, first2, last2, ... parameters which starts to become unwieldy if there are many authors. The advantage of using these parameters is they allow generation of clean metadata and allow the use of |display-authors=, |author-link=, etc. parameters. To permit the storage of author data in a more compact comma delimited list while retaining all the advantages of first1, last1, first2, last2, ... parameters, I created the {{vcite2 journal}} template (see also rationale). Boghog (talk) 06:51, 1 February 2015 (UTC)
Perhaps I might offer a comment? I suspect many editors prefer horizontal format (one long line) because it is more compact, does not split the text as much as vertical format does. What I would add here is that all the bibliographic detail that is proper for a full citation is always intrusive in the text, regardless of how it is formatted. There is much to be said for collecting all that detail in a special section, and linking to it from the text with "short" citations. This makes it a lot easier to edit the text, and a lot easier to edit citations (such as for consistency, etc.), because these two kinds of "text" are no longer intermingled. ~ J. Johnson (JJ) (talk) 22:53, 3 February 2015 (UTC)
Yes we had consensus to switch citations over many lines to citations over one line at WPMED. Doc James (talk · contribs · email) 04:02, 4 February 2015 (UTC)
I see this discussion has attracted more interest than I expected. I'd appreciate comments from all of you (knowing that you tend to work on articles in disciplines other than psychology, which is what I'm best equipped to work on) on my new guide to brief inline citations to specific pages in reliable sources used multiple times in one article. I learned that style from a much more experienced Wikipedian, and I'm looking forward to refining the style--with your advice--to improve many more high-page-view articles about psychology. -- WeijiBaikeBianji (talk, how I edit) 05:31, 4 February 2015 (UTC)
I use cite journal rather than Harvnb as I am not sure if the latter works in other languages.
But this is a personal preference. Doc James (talk · contribs · email) 07:03, 4 February 2015 (UTC)
In "other languages"? Why not? Perhaps you are thinking of special characters used in names? {{Harv}} was modified for those several years ago. I don't know if Unicode encodings work (may have to try that) but I believe Harv is compatible with all European names. ~ J. Johnson (JJ) (talk) 22:13, 4 February 2015 (UTC)
Because all these templates have not been installed in most languages. Doc James (talk · contribs · email) 11:40, 5 February 2015 (UTC)
Ah! That's not a language problem, but a problem with the wiki of a some language. More particularly, an incomplete installation of needed templates. ~ J. Johnson (JJ) (talk) 21:57, 5 February 2015 (UTC)

──────────────────────────────────────────────────────────────────────────────────────────────────── @WeijiBaikeBianji: Concerning the guide to brief inline citations, there are two methods that are in use in your example, both of which have distinct advantages and disadvantages. The is no one "best" way to organize citations. A lot depends on the type of citations and how they are used. Individual editors may also have their own preferences and which style is used is subject to WP:CITEVAR. In your example, the first citation style is {{harvnb}} and the second is List defined references. I think harvnb makes most sense if the citations are to books and different pages of same book are cited in different parts of the Wikipedia article. The disadvantage of this method is that it is more complicated and generally not needed if most of the citations are to journal articles. If different pages of the same source need to be cited, {{rp|page number(s)}} is an alternative. The advantage of list defined references is it separates the clutter of the citations from the text. The disadvantage is that it is separates the text from the source that supports that text make it somewhat more difficult to compare the two. List defined references make the most sense if the same source is used multiple times while less sense if each source is cited only once. Boghog (talk) 20:42, 5 February 2015 (UTC)

As Doc James mentioned above, another potential disadvantage of both techniques is that they may not be supported in all foreign language Wikipedias making it more complicate to transfer a English Wikipedia article's citations into a foreign language article. Boghog (talk) 21:06, 5 February 2015 (UTC)

I've already run into a wiki that runs Media Wiki software but without all the extensions used on English Wikipedia, so now I have a lot of interest in what minimal mark-up that might transfer to lots of different wikis would look like. I'd be best off looking at the Media Wiki documentation to understand that, I suppose? Thanks for the very interesting comments here. -- WeijiBaikeBianji (talk, how I edit) 21:32, 5 February 2015 (UTC)
Yes, identifying the extensions necessary for doing proper citations would be good. But should also look for any reason why these don't get installed. Starting to sound like a project. [Whoops! I thought I had signed this.] ~ J. Johnson (JJ) (talk) 00:25, 7 February 2015 (UTC)

Protein nomenclature[edit]

In light of your comments about the protein template merger, I figured you might have some thoughts on a protein naming problem. We currently have an article ribonuclease A, and another, skimpier one at pancreatic ribonuclease, to which RNase I redirects. Fine, except RNase A and RNase I and pancreatic ribonuclease are all accepted synonyms for the same thing. Worse, the UniProt recommended name for these in eukaryotes is the clunky "ribonuclease pancreatic". The RNase A article (the most common term in the literature by a long shot) focuses mostly on the well-studied bovine form (UniProt).

The technically correct resolution seems to be: merge the general content in ribonuclease A to pancreatic ribonuclease, redirect, and move what remains on the bovine protein to bovine ribonuclease pancreatic, but that's awful. Is there any compelling reason (broken bots?) not to put the bovine form at bovine pancreatic ribonuclease, even though that breaks the convention a bit? Opabinia regalis (talk) 07:35, 5 February 2015 (UTC)

@Opabinia regalis: Thanks for your note. I agree with your suggestion of merging ribonuclease A into pancreatic ribonuclease (the Enzyme Commission accepted name). WP:COMMONNAME would argue for a merger in the opposite direction, but I think consistency with the names of other enzyme articles which for the most part also use the EC name shifts the balance toward the EC name. Per WP:COMMONNAME, I would also support using the name bovine pancreatic ribonuclease since that is the one that is most commonly used (see below) and is less awkward sounding. Compare:
Boghog (talk) 20:09, 5 February 2015 (UTC)
Thanks, I'll sort these out when I get a chance. I noticed this when investigating some Pfam/Wikipedia mapping problems. (I do now think there are issues with the multiple infobox templates, but the problem seems to be using Template:Infobox enzyme, which has no Pfam parameter, for articles whose subjects really are families.) Opabinia regalis (talk) 00:09, 6 February 2015 (UTC)
@Opabinia regalis: As you are no doubt aware, the information contained in {{infobox enzyme}} which is based on Enzyme Commission numbers represent an enzymatic reaction, not an evolutionary related family of proteins. As a result of convergent evolution, two completely different protein folds may catalyze identical reactions and hence would be assigned the same EC number (see non-homologous isofunctional enzymes). As a consequence, the relationship between EC numbers and pfam families is not always one-to-one. Where they are one-to-one, I think it would be appropriate to add both an {{infobox enzyme}} and {{infobox protein family}} to the same article. When there is a single human gene that encodes an enzyme with a given EC number, it may also be appropriate to add a {{GNF Protein box}}, although this starts to become very messy and it may be better to keep the articles separate. One could think of some sort of a merged infobox which would have separate sections for a protein fold, evolutionary related genes that encode that fold, and enzymatic reactions catalyzed by that fold, but I think this merged box would be even more confusing for editors to create and maintain compared to using separate infoboxes. Boghog (talk) 11:21, 7 February 2015 (UTC)
PS: Good to see you back. We have missed you. Boghog (talk) 11:24, 7 February 2015 (UTC)
I was thinking along the lines of the switching parameters suggested in the merge discussion, as a way to streamline the display and encourage filling in as much information as available rather than just what's suggested in one set of infobox parameters. Right now it looks like most articles stop at one box (or where they do have two, as in ribonuclease H, there ought to be [at least] three). But you're right that that could create other confusions. For the time being I mostly just want the enzymes in common laboratory use to have accessible annotations.
Thanks, I don't know that I'm back for the long term, but might as well make myself useful. Strange how little has changed really. Opabinia regalis (talk) 23:29, 8 February 2015 (UTC)

Microscale thermophoresis[edit]

Hi! Sorry, I edited again since I thought I just missed to save... — Preceding unsigned comment added by SciMarie (talkcontribs) 16:30, 5 February 2015 (UTC)

No worries. Thanks for your note. Boghog (talk) 16:34, 5 February 2015 (UTC)

looks good! Thanks for you help and input! — Preceding unsigned comment added by SciMarie (talkcontribs) 16:36, 5 February 2015 (UTC)

NAD(P)H dehydrogenase (quinone 1)[edit]

The article is a stub so expanding the article with new information is necessary. If you delete new information you will prevent a coverage of the whole area of interest. If something is unclear or could be improved just expand it yourself or correct it. — Preceding unsigned comment added by 190.57.232.111 (talk) 18:28, 6 February 2015 (UTC)

@190.57.232.111: Your latest edit is much better since it emphasizes what the publication say about the enzyme and not what the enzyme says about the publication, but per WP:MEDRS, secondary sources are strongly preferred to support medical claims. The source that you have supplied (PMID: 21034357) is primary and needs to be replaced. Per WP:COI, Wikipedia is not the forum to promote your own publications. Boghog (talk) 20:06, 6 February 2015 (UTC)

Thank you for your help. It was the paper containing the crystal/NMR structure and the analysis of the data for the variant so it is the source for this specific data. I could not find another structure yet. Perhaps the other sources should be audited as well since there are two other primary sources too. Maybe all of the sources could be fortified (but not replaced) by this review :The NQO1 polymorphism C609T (Pro187Ser) and cancer susceptibility: a comprehensive meta-analysis [[2]]? — Preceding unsigned comment added by 190.57.232.111 (talk) 21:10, 6 February 2015 (UTC)

Image[edit]

Top: this graph depicts the acute expression of various Fos family proteins following an initial exposure to an addictive drug.
Bottom: this graph depicts ΔFosB expression following repeated drug exposure, where these phosphorylated ΔFosB isoforms persist in neurons for up to 2 months.

Hey Boghog, just wondering if you have any feedback before I paste this image into FOSB.
It came from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC58680/figure/F1/. Seppi333 (Insert  | Maintained) 07:18, 8 February 2015 (UTC)

Hi Seppi. The figure itself is fine. There may be a problem with copyright however. I noticed you raised the question here and did not get a clear answer. I don't think the X-ray example is a good analogy. A closer analogy can be made with chemical structure drawings that was discussed here. The conclusion was chemical structure drawings that are not "traced" are OK to used because of the merger doctrine where the "expression is considered to be inextricably merged with the idea". In your case, you are using an exact "traced" copy. The safest option of course would be to redraw the figure. The simplest way to draw the curves would be to use a Bézier curve which some versions of PowerPoint have (see for example [3] echosvoice). Another possibility is if you have a mathematical function that approximates the curves, one could plot it in Excel. I will play with this a bitl.
I also see that you have uploaded this figure to commons with the {{cc-by-3.0}} license. Because copyright laws differ between different countries (see Commons fair use), it would be safer to upload figure into the English language Wikipedia and claim fair use under US copyright law (rationale is that you have only copied a part of the figure). Alternatively you could ask permission from the publisher and submit a WP:OTRS. Boghog (talk) 10:04, 8 February 2015 (UTC)
@Seppi333: OK, I misunderstood and now see that you have redrawn it. However you use the word "trace" in the summary description. This description is problematic. If it is an exact trace, it does not get around the copyright issue. If it is redrawn without tracing, I would suggest that you change the word "trace" to "redrawn". I know this seems like a small semantic issue, but it can have legal repercussions. Boghog (talk) 10:11, 8 February 2015 (UTC)
I traced some the lines in the top graph - the rest I reproduced differently from the journal graphs. E.g., there are differences in the axis marks, text ("exposure"), text location, and graph cutoff point on the x-axis. I'll revise the description I guess. Seppi333 (Insert  | Maintained) 10:48, 8 February 2015 (UTC)
Edit: when I say "traced" I mean "manually fit a bezier curve through it until they lined up", in the event that's ambiguous. I can make some superficial tweaks if this is an issue though - just let me know. Seppi333 (Insert  | Maintained) 10:52, 8 February 2015 (UTC)
The change in the description is probably sufficient and I don't think any changes of the figure are needed. Boghog (talk) 05:54, 9 February 2015 (UTC)

Citation error introduced by substing[edit]

You appear to have introduced a citation error into Tobacco smoking when you replaced a cite PMID template with a cite journal content (see the last citation). I don't know how that could have happened if you were simply substing the templates. Be careful out there. – Jonesey95 (talk) 15:44, 8 February 2015 (UTC)

@Jonesey95: There were author parameter inconsistencies in the {{cite pmid/9862656}} and {{cite pmid/2136102}} templates that were substituted and the script I am using to do the substitution did not anticipate these inconsistencies could exist (these templates contained "author" + "first" + "last2" + "first2" parameters, huh?). I will modify the script so that it checks for inconsistent author format input and outputs a consistent author format. Please note that this script does a lot more than substitute the templates. It rebuilds the templates from scratch using the data supplied by the templates and supplements with data from PubMed if missing in the template. The script also checks to see what the predominate citation style is (multiple authors assigned to a single "author" parameter vs. "first1, last1, ..." parameters) and maintains that style in the substituted template. (Of course, it would be much cleaner to use the more compact {{vcite2 journal}} template and store the author list in the |vauthors= parameter ;-) Boghog (talk) 17:23, 8 February 2015 (UTC)
Thanks for updating the script. As far as I know, there are no cite doi or cite pmid templates with CS1 author-related errors; I try to keep the template space free of CS1 errors, although it is currently cluttered with "chapter= ignored" errors that will be fixed with a CS1 module update at the end of this week.
If your script is going to upgrade and improve the citations, not just subst them, you might want to scroll to the end of each article when it is in Preview mode after applying the script, then do a quick check for citation errors before you save. That's how I perform script-assisted edits, since editors put all sorts of crazy things into citations, and GIGO can lead to unexpected results. It just takes a few extra seconds. – Jonesey95 (talk) 18:29, 8 February 2015 (UTC)
That is the reason I am running the script for the time being manually to catch these sort of errors. I do visually look at the end of the article in preview to catch these errors, but for some reason, I missed this one. Eventually the intention is to have a bot run the script after it is sufficiently debugged. Boghog (talk) 18:36, 8 February 2015 (UTC)

Removing information[edit]

I'm sorry I've felt it necessary to revert your recent edit to Hyperbaric medicine. I'm very sympathetic to the desire to do away with {{cite doi}} and removing access dates from journals, but your edit went far beyond that. You changed dates with month and year to just the year. You merged multiple author parameters into a single author parameter. You replaced the full name of a journal with an abbreviation. In each of these cases your edit removed information, or reduced data granularity, or obfuscated information. The data in our references is available for third parties to use via data dumps and removing pieces of information or lumping together multiple pieces of information simply makes it more difficult for those third parties to extract information from the dumps. Someone had gone to the trouble of separating individual editors when writing the reference and you ditch that hard work when you pull all of it into the author parameter - not to mention that you make the reference less amenable for re-use in other articles that use different citation styles because you've hard-coded the separators. Finally there's a long-standing consensus that because this is not a paper encyclopedia, it's better not to use journal abbreviations (Wikipedia:Scientific citation guidelines #Citation format); many readers won't know the abbreviations and supplying the full journal title is a service to them. Again, somebody went to the trouble of finding the full journal title and using it. Setting it back to an abbreviation is a retrograde step and you ought to avoid doing that. --RexxS (talk) 01:08, 11 February 2015 (UTC)

Should be fairly easy to use the full journal name and the year and month yes? Doc James (talk · contribs · email) 05:50, 11 February 2015 (UTC)
Also for the ref width can we go with 32 rather than 35? 35 just gives me one column rather than two. Doc James (talk · contribs · email) 06:31, 11 February 2015 (UTC)

──────────────────────────────────────────────────────────────────────────────────────────────────── @RexxS::

  • multiple author parameters into a single author parameter – The original consensus stated that the substitution of {{cite pmid}} templates should comply with WP:CITEVAR. Concerning the author parameters, my edits were completely consistent with WP:CITEVAR. The Hyperbaric medicine article had a mix of author formats but by far the predominant (and the originally established style) stored a Vancouver style comma separated author list in a single |author= parameter (70 citations). In addition six citation used "first, last, author2, author3, ..." format, four used a deprecated "coauthor " format, and one was a transcluded {{cite pmid}} citation that used a "first1, last1, first2, last2, ..." format. WP:CITEVAR also states that consistent a citation style within an article is desirable. Before my edits, there was a mix of styles. After my edit, there was a consistent style. The reason for using "first1, last1, first2, last2, ..." parameters is that it generates clean metadata. However the value of this metadata is highly dubious. First, how often is this used? Second, Wikipedia is not a reliable source and this includes citations that may suffer from accidentally or intentionally introduced errors. The vast majority of this citations in this article came from PubMed. The only metadata one really needs is the pmid where one can download a fresh, error free copy using RefToolbar or some similar tool. The best long term solution might be to use a parameter like |vauthors= in {{vcite2 journal}} that would generate clean metadata without the character overhead of explicit "first1, last1, first2, last2, ..." parameters (see rationale).
  • Someone had gone to the trouble of separating individual editors when writing the reference – that someone was Citation Bot (diff) as a followup to an incomplete citation added by an ip (diff). This bot edit was in violation of WP:CITEVAR.
  • reduced data granularity – I reduced excessive unnecessary data granularity. The Vancouver style comma separated author list is trivial to parse.
  • simply makes it more difficult for those third parties to extract information from the dumps – again, before my edit there was an inconsistent mix of formats. After my edit, there was a consistent format that makes it easier to extract information.
  • your edit removed information – some of the citation author lists were incomplete and my edit added the missing authors. Again, why would anyone want to reuse incomplete error prone citation data extracted from a Wikipedia article? Wikipedia is not a reliable source of citation data. PubMed is.
  • full name of a journal with an abbreviation – again, the reason for doing this was consistency. The majority of citations before my edit used abbreviations. I can modify the script so that full journal names are used throughout. However the danger of doing this is that occasionally a journal has a very long name in which case other editors might complain.
  • month and year to just the year – once again for consistency. I can modify the script so that a consistent |date=MMM YYYY format is used.

I hope this explanation is sufficient. Would it be acceptable to use a consistent (1) Vancouver style author format, (2) full journal names, and (3) |date=MMM YYYY throughout this article? Boghog (talk) 15:13, 11 February 2015 (UTC)

I understand your rationale, but I still think it's sub-optimal in respect of the author parameter.
I often reuse citations in related articles, but sometimes find that the citation style is different. Using the last1, first1 format allows any citation to be immediately reused and has absolutely no disadvantage compared to the hard-coded author format which requires changing by hand.
You also may call this level of data granularity "unnecessary"; I say it's not and I don't think you have any evidence that supports your assertion.
Similarly, questioning the value of our data to third parties doesn't favour your change to author format as that is just as prone to error, yet requires an extra stage of parsing that isn't needed with the first, last format. First, last has nothing but advantages over author format and I repeat that it degrades the quality of the information to move away from that. Google is known to make extensive use of our data dumps, for example, despite the occasional error, because it's the largest, decent quality source of both structured data and free text. If you ever find a hour to spare, I'd recommend viewing "Intelligence in Wikipedia" as you may be surprised at what uses our data is put to.
WP:CITEVAR is much misused to bolster one side of a disagreement, so it may be worth examining what it actually says. It says that citations should not be changed between two equivalent styles - this is to stop back-and-forth edit wars between say API and Vancouver simply because of editor preference. It does not prohibit upgrading the references; the extreme case of from bare urls to citation templates being an obvious example. In addition, the method of determining which style to consolidate to when there is a mixture of incompatible styles is to be determined by the style used by the first major contributor, not by taking a numeric count (even though the latter is more convenient). In brief, if you're going to ignore CITEVAR anyway, why not simply consolidate all cites to the superior last, first format which is at least defensible as an upgrade?
Finally, I'd like to express my appreciation of the work you're doing in improving references here. My dissent over the detail is meant to be wholly constructive as I think there is an opportunity to do an even better job. I won't revert you further whatever you decide in going forward. Cheers --RexxS (talk) 16:49, 11 February 2015 (UTC)
Thanks for your thoughtful reply. A couple of thoughts in response:
  • Copying a "last1, first1, ..." formatted citation into another article that uses Vancouver style citations introduces formatting inconsistencies.
  • The disadvantage of the "last1, first1, ..." format is parameter bloat and the increase in size of the template. This makes it harder to spot and edit prose that the citation is imbedded into.
  • Extracting the pmid from a citation and inserting the same citation with RefToolbar is less error prone than copying a citation from one article into another. As a specific example, the Hyperbaric medicine article had several citation templates that had missing authors (PMID: 22592699, 11558483, 16299259, 18643783, and 19485935) and one that contained a misspelled journal name (PMID: 6159432). By copying these citation templates into another article, these errors would have been propagated. By inserting the pmid into RefToolbar to create the citation from scratch, these errors would have been corrected.
  • First addition of citations to the Hyperbaric medicine article in the were in this edit, which itself was internally inconsistent, but at least half were in Vancouver format. First in-line citation were in this edit. The first templated citations were added in this edit and used Vancouver formatted authors in single |author= parameter. Hence not only the current predominate format, but the first established format used the Vancouver system. This is probably true of most older medical articles that used Diberri's template filling tool to create citations.
  • Module:ParseVauthors that is used by {{vcite2 journal}} is strong evidence that "last1, first1, ..." data granularity is not necessary. This is a very efficient Lua module that rapidly and accurately parses |vauthors= parameter contents with appropriate error checking to produce clean author metadata and is fully compatible with |author-link= and |displayauthors= parameters. Furthermore its use is completely transparent to both Wikipedia editors and content consumers.
  • Which citation format is superior is a matter of opinion. IMHO, the best long term solution would be to add |vauthors= support directly into Module:Citation/CS1 so that it can be used in the standard {{cite journal}}, {{cite book}}, etc. templates. This parameter would have all the advantages of "last1, first1, ..." parameters without the character overhead which can become significant for citations with a large number of authors. Boghog (talk) 20:57, 11 February 2015 (UTC)
And thank you for your thoughtful response. Sadly my principal interest is in scuba diving (and thence hyperbaric medicine), so I don't always get sources with a pmid. The one remaining issue that I'd comment on is the problem of citations obscuring the text where they are embedded. I'm a strong advocate of using list defined references once an article has stabilised to "de-snot" the text as a wiki-friend of mine was fond of calling it. Obviously once references are placed in the References section - where they belong - you don't have to worry about bloat. One day we'll use just the {{sfn}} and {{r}} templates within the text and editing scientific & medical articles will become easy again. Regards --RexxS (talk) 23:31, 11 February 2015 (UTC)

about my link[edit]

Hi, boghog I did read the guidelines and policy and I must have missed a few things, when you pointed me in the right direction I saw that the like that I posted did in fact violate the terms and conditions.

That was not my intention as I thought it was relevant and is except for the fact that it's also there to sell which is the part that violates the terms and conditions.

I do apologize for this and will try to pay more attention to what is allowed and not allowed as I am new here.

Sincerely, Matt6648 — Preceding unsigned comment added by Matt6648 (talkcontribs) 18:43, 15 February 2015 (UTC)

Thanks for your note and welcome to Wikipedia! I do appreciate that you carefully read the terms and now understand them. I wish more people had your constructive and positive attitude. Cheers. Boghog (talk) 20:16, 15 February 2015 (UTC)

Tagging as reviews / primary[edit]

I like this a lot. Thanks for doing it. Doc James (talk · contribs · email) 20:57, 18 February 2015 (UTC)

@Doc James: Thanks. I noticed someone else included these designations in the original non-templated citations and I wanted to preserve these. You might be interested in this discussion when we tried to decide the best {{cite journal}} parameter to use this purpose. The discussion got side tracked on whether including such a designation is original research or not. I obviously don't think so, but others disagree. I would appreciate you input. On practical matter the |department= parameter is both a non-obvious (i.e., the name of a "department" in a magazine or newspaper) and not ideal since it doesn't automatically include parenthesis. Boghog (talk) 16:21, 19 February 2015 (UTC)

Spam?[edit]

I appreciate where you are coming from. However, the entire goal of an open source reference is to encourage individuals to add material where they have specific knowledge. I sincerely hope that you and others will edit, remove and improve what I have tried to add, however, a blanket declaration of 'spam' is not right, nor an accurate description. — Preceding unsigned comment added by Jon33dn (talkcontribs) 23:25, 20 February 2015 (UTC)

@Jon33dn: Repeatedly adding citations authored by one research group to a number of articles in a short period of time is definitely ref spam. If you have any connection to the authors of these citations, adding these citations represents a conflict of interest. Please note that excessive self-citation is strongly discouraged. Thank you. Boghog (talk) 23:32, 20 February 2015 (UTC)
@Boghog: I would ask that you and any other future edits focus on the actual content added. Good faith addition of content is not spam, nor a conflict of interest.
@Jon33dn: To reiterate, you have added a number of citations from the same research group to a number of articles:
This strongly suggests to me that you have a conflict of interest. Futhermore secondary sources (i.e., review articles) are preferred over primary. Even though primary sources may have been peer reviewed, secondary sources are generally preferred over primary because it is an independent verification that the source is notable, and is a second check as to the reliability of the conclusions as a disturbingly large number of research results cannot be reproduced. Boghog (talk) 23:39, 20 February 2015 (UTC)
@Boghog: I think we shall simply disagree. Respect for your efforts. The content added is obviously the same set of results in the various appropriate locations where it is topical. Suggestion to add to the talk page is a welcome piece of information.
@Jon33dn: The issue here is more than a disagreement between two editors. WP:SELFCITE is a Wikipedia policy that states in part Using material you have written or published is allowed within reason, but only if it is relevant, conforms to the content policies ... is not excessive ... and should not place undue emphasis on your work. When in doubt, defer to the community's opinion. I am part of the community opinion. You have only added citations from one research group to a number of articles which clearly qualifies as excessive. Furthermore all the citation you have added are WP:PRIMARY (reliable primary sources may be used in Wikipedia; but only with care, because it is easy to misuse them). Citing only your own papers is neither acceptable in scientific publications nor per WP:UNDUE, in Wikipedia. Finally the material that you have added appears not central to the subject of the article. In short, the purpose of the material that you have added appears more to promote the work of one research group rather than improve Wikipedia. Boghog (talk) 00:08, 21 February 2015 (UTC)
@Boghog: Actually, I think a disagreement it is exactly what it is. I am also a part of community opinion and I believe the content I have added is valuable to the topics where they were posted. I also assert that my use of citations are within reason and relevant. Nor are they excessive as they support the statements made. Addition of more and diverse citations by yourself would not be amiss.

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